ivar calls three nucleotide changes instead of just one complete codon change

[saramonzon]

Hi!
Thanks for the tool! We use it on nf-core/viralrecon pipeline as you may know, which is being mainly used for SARS-Cov-2 analysis. We've noticed that complex variants as a the triplet nucleotide change which change the entire codon in the uk variant of concern, ivar reports three nucleotide changes instead of just one, with the subsequent wrong aminoacid annotation.
Do you think this could be implemented for ivar to detect this as just one variant instead of three?

[gkarthik]

This is a very good point. Thank you!
I need to think more about how to do this but this will be very critical.